Thank you for the reply,
1. I'm not sure. I use the CycloneII dev-kit with the components as created by Altera. I'm lokking into it...
2. If I understand it correctly I am doing excatly that. The code I used to program the EPCS is:
sof2flash --input=/cygdrive/t/CSC/Lusdetector_onderzoek_PV04900/03-0032-1_Lusdetector_usb_noFlash/fpga/standard.sof --output=standard.flash --epcs
elf2flash --epcs --after=standard.flash --input=../kits/nios2/bin/eclipse/workspace/kernel_no_flash/build/vmlinux --output=vmlinux.flash --boot=boot_loader_epcs.srec --end=0x3ffffff
nios2-flash-programmer --epcs --sof=altera_nios_dev_board_cyclone_2c35.sof --input=standard.flash
nios2-flash-programmer --epcs --sof=altera_nios_dev_board_cyclone_2c35.sof --input=vmlinux.flash --relocate
from the documentation I thought the bootloader I include when generating the vmlinux.flash file sits in the first 1K (which is directly accesable) and copies the vmlinux to ram and jumps to the start-address.